Two years have passed since the final battle with Sephiroth. Though Midgar, city of mako, city of prosperity, has been reduced to ruins, its people slowly but steadily walk the road to reconstruction. However, a mysterious illness called Geostigma torments them. With no cure in sight, it brings death to the afflicted, one after another, robbing the people of their fledgling hope.

After the destruction of Nibelheim at the hands of Sephiroth, Zack and Cloud are on the run from Shinra Inc. As they make their way back to Midgar, they recall the horrible events that happened at Nibelheim, as well as fight for survival against Shinra.

It's been four years since Meteor fell on Midgar. Denzel meets Reeve at an outskirts coffee shop about joining the World Regenesis Organization. Upon the request Denzel tells Reeve about what his life was like prior to the Meteor incident.